import SimpleITK as sitk
import matplotlib.pyplot as plt
from matplotlib.widgets import Slider
import numpy as np


Files = ['/home/morrile2/Documents/MULTIS Data/MRI_LEG_113016/16 AX t1_2MMSLICE_1MMGAP_FEMUR1_OVERLAP_25SLICES.nii',
'/home/morrile2/Documents/MULTIS Data/MRI_LEG_113016/17 AX t1_2MMSLICE_1MMGAP_FEMUR2_25SLICES.nii',
'/home/morrile2/Documents/MULTIS Data/MRI_LEG_113016/18 AX t1_2MMSLICE_1MMGAP_FEMUR3_25SLICES.nii']

reader = sitk.ImageFileReader()
reader.SetFileName(Files[0])
img_1 = reader.Execute()
# x, y, z = img_1.GetSize()
# img_1 = sitk.RegionOfInterest(img_1, size = (x, y, z-10), index = (0,0,10))

reader = sitk.ImageFileReader()
reader.SetFileName(Files[1])
img_2 = reader.Execute()
# x, y, z = img_2.GetSize()
# img_2 = sitk.RegionOfInterest(img_2, size = (x, y, z-10), index = (0,0,10))

reader = sitk.ImageFileReader()
reader.SetFileName(Files[2])
img_3 = reader.Execute()
# x, y, z = img_3.GetSize()
# img_3 = sitk.RegionOfInterest(img_3, size = (x, y, z-10), index = (0,0,10))

# reader = sitk.ImageFileReader()
# reader.SetFileName(Files[3])
# img_4 = reader.Execute()
# x, y, z = img_4.GetSize()
# img_4 = sitk.RegionOfInterest(img_4, size = (x, y, z-10), index = (0,0,10))

# reader = sitk.ImageFileReader()
# reader.SetFileName(Files[4])
# img_5 = reader.Execute()
# # x, y, z = img_5.GetSize()
# # img_5 = sitk.RegionOfInterest(img_5, size = (x, y, z-10), index = (0,0,0))

img_comb = sitk.TileImageFilter()
img_comb.SetLayout((1,1,0))
img_comb3 = img_comb.Execute(img_3, img_2, img_1)


sitk.WriteImage(img_comb3, '/home/morrile2/Documents/MULTIS Data/MRI_LEG_113016/MRI_trial4_seq2_25slice_2mmslice_1mmgap.nii')